The micro USB connector on the APM boards is extremely fragile and easily damaged.
My solution was to insert a Micro USB to Mini USB adapter to the copter:
Here's an example:
Do not try to use a similar appearing charger adapter. They typically lack the data wires.
On the other hand, I do use a USB charger to power the APM without connecting the LiPo. This lets me safely communicate with the APM over the 3DRadio.